Software

Image processing and analysis software

CELLIM provides commercial and open-source software for microscopy image processing, bioimage analysis, image visualisation and quantitative data analysis. The main software environment is available on the remote Odeon image processing server. Galibier remains available as a local backup workstation when Odeon is fully booked.

CELLIM is part of the Euro-BioImaging network, which makes CELLIM imaging and bioimage analysis services accessible to users from around the world. Thanks to this open-access infrastructure and Odeon's remote RDP access, users can work with CELLIM image processing resources from outside CEITEC and from abroad.

Workstations overview  |  Odeon  |  Galibier  |  Booking system  |  CELLIM contact form  |  Euro-BioImaging

		Software name	Available on
			Galibier	Odeon
		ZEN Blue and ZEN Black Zeiss image processing, deconvolution, Airyscan processing and advanced image analysis. Odeon currently provides ZEN Blue 3.12 and ZEN Black 3.0 SR; Galibier provides older ZEN versions.	✓	✓
		Imaris 3D/4D microscopy image visualisation and analysis software for segmentation, tracking, colocalization and quantitative bioimage analysis. Odeon currently provides Imaris 11.0.1; Galibier provides an older full version.	✓	✓
		Imaris Viewer Viewer for Imaris datasets and IMS files.	✓	✓
		CellProfiler Automated and batch image analysis pipelines for high-throughput bioimage analysis.	✓	✓
		Fiji Open-source image processing package based on ImageJ, with many plugins and macro workflows for microscopy image analysis.	✓	✓
		LAS X Leica software for processing and analysis, viewing and exporting images. Odeon includes LAS X with LIGHTNING deconvolution and LAS X Single Molecule Detection for FLIM-related analysis.		✓
		Evident CellSens Evident/Olympus microscopy image viewing, processing and analysis.	✓
		Cellpose AI-based cell and nucleus segmentation for microscopy images.	✓

Recommended use

Use Odeon for large microscopy datasets, high-throughput image processing, remote image analysis, Imaris 11 analysis, Zeiss ZEN processing, CellProfiler batch analysis, Fiji/ImageJ workflows, Leica LIGHTNING deconvolution and FLIM-related LAS X analysis.

Use Galibier when you need a local image processing workstation, when Odeon is fully booked, or when you want to inspect data and develop analysis workflows on site.

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